Hmm, I would be a bit skeptical of that figure without observing incorporated city limits and how far out they extend. Sometimes population figures include the "metro area" as well.
This is a very good point, as there are western regions of Tokyo that after much lower density than central Tokyo. A good measure may be to look at the density in Minato-ku.
Minato has a population density of 10850/km2, Shinjuku of 18500/km2, Meguro of 18900/km2, and Nakano wins out at 20,700/km2. (Nakano winning surprised me. It's pretty low-rise for Tokyo!)